Microbial Enemies Research Articles

Uncovering the genomic basis of an extraordinary plant invasion.

Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant’s remarkable success as an invasive species.

Transcriptomic Insights into the Insect Immune Response to Nematode Infection.

Insects in nature interact with a wide variety of microbial enemies including nematodes. These include entomopathogenic nematodes that contain mutualistic bacteria and together are able to infect a broad range of insects in order to complete their life cycle and multiply, filarial nematodes which are vectored by mosquitoes, and other parasitic nematodes. Entomopathogenic nematodes are commonly used in biological control practices and they form excellent research tools for understanding the genetic and functional bases of nematode pathogenicity and insect anti-nematode immunity. In addition, clarifying the mechanism of transmission of filarial nematodes by mosquitoes is critical for devising strategies to reduce disease transmission in humans. In all cases and in order to achieve these goals, it is vital to determine the number and type of insect host genes which are differentially regulated during infection and encode factors with anti-nematode properties. In this respect, the use of transcriptomic approaches has proven a key step for the identification of insect molecules with anti-nematode activity. Here, we review the progress in the field of transcriptomics that deals with the insect response to nematode infection. This information is important because it will expose conserved pathways of anti-nematode immunity in humans.

Very Short and Stable Lactoferricin-Derived Antimicrobial Peptides: Design Principles and Potential Uses.

The alarming rate at which micro-organisms are developing resistance to conventional antibiotics represents one of the global challenges of our time. There is currently ample space in the antibacterial drug pipeline, and scientists are trying to find innovative and novel strategies to target the microbial enemies. Nature has remained a source of inspiration for most of the antibiotics developed and used, and the immune molecules produced by the innate defense systems, as a first line of defense, have been heralded as the next source of antibiotics. Most living organisms produce an arsenal of antimicrobial peptides (AMPs) to rapidly fend off intruding pathogens, and several different attempts have been made to transform this versatile group of compounds into the next generation of antibiotics. However, faced with the many hurdles of using peptides as drugs, the success of these defense molecules as therapeutics remains to be realized. AMPs derived from the proteolytic degradation of the innate defense protein lactoferrin have been shown to display several favorable antimicrobial properties. In an attempt to investigate the biological and pharmacological properties of these much shorter AMPs, the sequence dependence was investigated, and it was shown, through a series of truncation experiments, that these AMPs in fact can be prepared as tripeptides, with improved antimicrobial activity, via the incorporation of unnatural hydrophobic residues and terminal cappings. In this Account, we describe how this class of promising cationic tripeptides has been developed to specifically address the main challenges limiting the general use of AMPs. This has been made possible through the identification of the antibacterial pharmacophore and via the incorporation of a range of unnatural hydrophobic and cationic amino acids. Incorporation of these residues at selected positions has allowed us to extensively establish how these compounds interact with the major proteolytic enzymes trypsin and chymotrypsin and also the two major drug-binding plasma proteins serum albumin and α-1 glycoprotein. Several of the challenges associated with using AMPs relate to their size, susceptibility to rapid proteolytic degradation, and poor oral bioavailability. Our studies have addressed these issues in detail, and the results have allowed us to effectively design and prepare active and metabolically stable AMPs that have been evaluated in a range of functional settings. The optimized short AMPs display inhibitory activities against a plethora of micro-organisms at low micromolar concentrations, and they have been shown to target resistant strains of both bacteria and fungi alike with a very rapid mode of action. Our Account further describes how these compounds behave in in vivo experiments and highlights both the challenges and possibilities of the intriguing compounds. In several areas, they have been shown to exhibit comparable or superior activity to established antibacterial, antifungal, and antifouling commercial products. This illustrates their ability to effectively target and eradicate various microbes in a variety of settings ranging from the ocean to the clinic.

Fungi on Commelina benghalensis from Brazil, with notes on potential for weed biological control

Commelina benghalensis (tropical spiderwort - TS) is an invasive herbaceous plant, native to South and Southeast Asia and one of the worst agricultural weeds in the tropics. Its management is notoriously difficult because of its ability to regenerate from small fragments and its tolerance to glyphosate applications. There are no published records of biocontrol attempts against TS involving either microbial or arthropod natural enemies. Prior to investigating classical biocontrol agents, surveys have been conducted in Brazil and, more recently, concentrated in Vicosa (state of Minas Gerais) to determine whether fungal pathogens of TS are already present. Five different fungal pathogens were collected. These fungi were identified as causing the following diseases: Athelia rolfsii – crown rot, Cercospora cf. sigesbeckiae – leaf spots, Corynespora cassiicola – leaf spots, Neopyricularia obtusa sp. nov. – leaf spots and Rhizoctonia solani – blight. One of the fungi found on TS represents a new taxon, and the others represent either a new host association, a new geographic record or both, except for Corynespora cassiicola, which has already been recorded as able to attack TS (ex-tomato isolates, under controlled conditions) in Brazil. The mycobiota identified in Brazil is limited and lacks many of the TS-specific fungal pathogens recorded in Africa and Asia, namely: Kordyana celebensis, Kordyana indica, Phakopsora tecta, Puccinia commelinae, Uredo ochracea, Bauerago combensis and Bauerago commelinae. It is conjectured here, that such exotic fungi, may offer a valuable resource for management of one of the worst agricultural weeds in Brazil and in the tropical world, and require investigation as biological control agents for introduction in Brazil.

The De Novo Synthesis of Horsepox Virus: Implications for Biosecurity and Recommendations for Preventing the Reemergence of Smallpox.

In March 2017, the American biotech company Tonix announced that a Canadian scientist had synthesized horsepox virus as part of a project to develop a safer vaccine against smallpox. The first de novo synthesis of an orthopoxvirus, a closely related group of viruses that includes horsepox and the variola virus that causes smallpox, crosses an important Rubicon in the field of biosecurity. The synthesis of horsepox virus takes the world one step closer to the reemergence of smallpox as a threat to global health security. That threat has been held at bay for the past 40 years by the extreme difficulty of obtaining variola virus and the availability of effective medical countermeasures. The techniques demonstrated by the synthesis of horsepox have the potential to erase both of these barriers. The primary risk posed by this research is that it will open the door to the routine and widespread synthesis of other orthopoxviruses, such as vaccinia, for use in research, public health, and medicine. The normalization and globalization of orthopoxvirus synthesis for these beneficial applications will create a cadre of laboratories and scientists that will also have the capability and expertise to create infectious variola virus from synthetic DNA. Unless the safeguards against the synthesis of variola virus are strengthened, the capability to reintroduce smallpox into the human population will be globally distributed and either loosely or completely unregulated, providing the foundation for a disgruntled or radicalized scientist, sophisticated terrorist group, unscrupulous company, or rogue state to recreate one of humanity's most feared microbial enemies. The reemergence of smallpox-because of a laboratory accident or an intentional release-would be a global health disaster. International organizations, national governments, the DNA synthesis industry, and the synthetic biology community all have a role to play in devising new approaches to preventing the reemergence of smallpox.

The hygiene hypothesis: identifying microbial friends and protecting against microbial enemies

We frequently read about how we have 'become too clean for our own good' - but is this really true? What is meant by this anyway? And, more importantly, what are the implications for hygiene and public health? This issue has been reviewed in a recent report by the International Scientific Forum on Home Hygiene (IFH).^sup 1,2^ Sally Bloomfield, Chairman of the International Scientific Forum on Home Hygiene and Visiting Professor, London School of Hygiene and Tropical Medicine, takes a closer look at the discussion.The hygiene hypothesis dates back to 1989, when Strachan proposed that a lower incidence of infection in early childhood could be an explanation for the rapid 20th century rise in allergic diseases. Over the last decade, researchers have recognised that the concept of a link between microbial exposure and allergy is probably correct, but the idea that children who have more infections are less likely to develop allergies is wide of the mark. Their other finding, which highlights the growing importance of this issue, is that the concept applies to a much broader range of chronic inflammatory diseases (CIDs) such as type 1 diabetes and multiple sclerosis, and also some types of depression and cancer.In 2003, Graham Rook proposed the 'Old Friends' hypothesis, which seems to offer a more rational explanation. He argues that the vital exposures are not colds, influenza, measles and other common childhood infections which have evolved relatively recently over the last 10,000 years, but rather the microbes already present over 2 million years ago in hunter-gatherer times when the human immune system was developing. His argument is that we have become so dependent on our 'Old Friends' that our immune systems cannot function properly without them.What sort of microbes do we need and when?Rook suggests that our 'Old Friends' are most likely to include the following:* Environmental species which inhabit our indoor and outdoor environments;* The normal microbiota of the human skin, gut and respiratory tract, and that of the animals we live with;* And organisms such as hepatitis A virus and helminths (worms) which establish chronic infections or carrier states, and that need to be tolerated.Studies now show how exposure to these microbes is vital because they interact with regulatory systems which keep our immune systems in balance. Without this our immune systems may react inappropriately, sometimes overreacting and causing asthma and hay fever, and sometimes attacking our own tissues and causing autoimmune diseases such as multiple sclerosis. Increasingly, it seems that diversity of exposure to these microbes is key to building a well-regulated immune system.For allergic disease, it seems that the most important times for exposure are early in development, during pregnancy and the first few days or months of infancy, and this exposure needs to be maintained over a significant period. This fits with evidence that Caesarean section may be associated with an increased tendency to develop allergies, while breastfeeding for 6 months or more can be protective. What we do not know is the extent to which exposures need to be maintained during childhood and adult life and whether these diseases could be contained or reversed by ongoing exposure. There is some evidence for this, but much more research is required to better understand.Are other factors involved?It now seems clear that the risk of allergic and other CIDs also depends on factors such as changes in diet, pollution, physical activity, obesity, socio-economic factors and stress. Genetic predisposition is also an influencing factor, which could explain why we do not all suffer from these diseases. We all still get some microbial exposure, which for some is sufficient, for others not. For these people, allergies and other CIDs may be triggered, when these other factors cause further immune dysregulation. …

Pseudomonas aeruginosa Adaptation to Lungs of Cystic Fibrosis Patients Leads to Lowered Resistance to Phage and Protist Enemies

Pathogenic life styles can lead to highly specialized interactions with host species, potentially resulting in fitness trade-offs in other ecological contexts. Here we studied how adaptation of the environmentally transmitted bacterial pathogen, Pseudomonas aeruginosa, to cystic fibrosis (CF) patients affects its survival in the presence of natural phage (14/1, ΦKZ, PNM and PT7) and protist (Tetrahymena thermophila and Acanthamoebae polyphaga) enemies. We found that most of the bacteria isolated from relatively recently intermittently colonised patients (1–25 months), were innately phage-resistant and highly toxic for protists. In contrast, bacteria isolated from long time chronically infected patients (2–23 years), were less efficient in both resisting phages and killing protists. Moreover, chronic isolates showed reduced killing of wax moth larvae (Galleria mellonella) probably due to weaker in vitro growth and protease expression. These results suggest that P. aeruginosa long-term adaptation to CF-lungs could trade off with its survival in aquatic environmental reservoirs in the presence of microbial enemies, while lowered virulence could reduce pathogen opportunities to infect insect vectors; factors that are both likely to result in poorer environmental transmission. From an applied perspective, phage therapy could be useful against chronic P. aeruginosa lung infections that are often characterized by multidrug resistance: chronic isolates were least resistant to phages and their poor growth will likely slow down the emergence of beneficial resistance mutations.

Interactions between nematodes and their microbial enemies in coastal sand dunes

European foredunes are almost exclusively colonised by Ammophila arenaria, and both the natural succession and the die-out of this plant have been linked to populations of plant-parasitic nematodes (PPN). The overarching aim of this study was to investigate top-down control processes of PPN in these natural ecosystems through comparative analyses of the diversity and dynamics of PPN and their microbial enemies. Our specific aims were, first, to identify and quantify PPN microbial enemies in European sand dunes; second, to assess their life history traits, their spatial and temporal variation in these ecosystems, and third, to evaluate their control potential of PPN populations. This was done by seasonal sampling of a range of sites and making observations on both the nematode and the microbial enemy communities in rhizosphere sand. Nine different nematode microbial enemies belonging to different functional groups were detected in European sand dunes. Their high diversity in these low productivity ecosystems could both result from or lead to the lack of dominance of a particular nematode genus. The distribution of microbial enemies was spatially and temporally variable, both among and within sampling sites. Obligate parasites, either with low host-specificity or having the ability to form an environmentally resistant propagule, are favoured in these ecosystems and are more frequent and abundant than facultative parasites. Three microbial enemies correlated, either positively or negatively, with PPN population size: Catenaria spp., Hirsutella rhossiliensis and Pasteuria penetrans. Microbial-enemy supported links in the food-web may be involved in the control of PPN populations through indirect effects. The endospore-forming P. penetrans was the most successful top-down control agent, and was implicated in the direct control of Meloidogyne spp. and indirect facilitation of Pratylenchus spp. Overall, our findings suggest strong and diverse top-down control effects on the nematode community in these natural ecosystems.

Mesocosm experiments to assess the transmission of Pandora neoaphidis within simple and mixed field margins and over the crop-margin interface

Although considerable research on the development of agri-environment schemes has focussed on the value of managed field margins as reservoirs for arthropod natural enemies, their potential as reservoirs of entomopathogenic fungi has received less attention. Whether field margins that are most beneficial for arthropod natural enemies are the same as those for entomopathogenic fungi is unknown. Here, within glasshouse mesocosms, we assessed the reproductive success of the aphid-specific entomopathogenic fungus Pandora neoaphidis on aphids in a ‘simple margin’ containing one plant species and on the same species of aphid in a ‘mixed margin’ containing seven plant species. These assessments were done in the presence of Aphidius ervi, a hymenopteran parasitoid of aphids regarded as being a key species to conserve in agri-environment schemes in the UK. When only the plants initially infested with aphids were assessed, transmission of P. neoaphidis was significantly greater (p<0.001) in the mixed margin as was parasitisation by A. ervi (p<0.05). However, when all of the plants in the mesocosms were assessed, transmission of P. neoaphidis remained greater in the mixed margin (p<0.05) whereas parasitisation by A. ervi was greater in the simple margin (p<0.05). This difference may be due to aphid dispersal which was greater in the simple margin thereby benefitting the actively foraging parasitoid whereas clustering of aphids in the mixed margin benefited the passively dispersed fungus. In a second mesocosm experiment, the movement of P. neoaphidis over the crop-margin interface was similar to that of A. ervi despite the fungus only being passively dispersed in contrast to the actively foraging parasitoid. The results presented here indicate that, although the optimal plant composition of field margins may differ for P. neoaphidis and A. ervi, both species can co-exist and reproduce in field margins and will move over the crop-margin interface. Managed field margins that benefit both key arthropod and key microbial enemies have potential for enhancing pest control in associated crops.

Local variation in belowground multitrophic interactions

A growing number of studies point at the involvement of root herbivores in influencing plant performance, community composition and succession. However, little is known about the factors that control root herbivore abundance and the role of local variation in the effectiveness of these factors. Here, we performed a full factorial experiment with plants, root-feeding nematodes and rhizosphere microbial communities from two dune sites, to test the hypothesis that the outcome of belowground multitrophic interactions depends on local differences between the interacting organisms. The organisms included the marram grass Ammophila arenaria, the cyst nematode Heterodera arenaria, microbial plant pathogens and natural enemies of the nematodes from two coastal foredune systems, one in The Netherlands and one in Wales. The two plant populations differed at the molecular and phenotypic level, and the microbial communities from the two dune sites differed in the composition of the dominant soil fungi but not of the dominant bacteria. Plants were negatively affected by the rhizosphere microorganisms from one of the sites. Nevertheless, nematode performance was not affected by the origin of both the host plants and the microbial communities. The reproductive output of the cyst nematode depended on the presence of microorganisms, as well as on inter-population variability in the response of the nematode to these natural enemies. In the absence of microorganisms, the two nematode populations differed in the number and size of the produced cysts, although maternal effects cannot be excluded. Inter-population differences in the host plant were a secondary factor in the nematode–microorganisms interactions, and did not influence bottom–up control of the cyst nematodes. Our results did not reveal strong signals of coevolution in belowground multitrophic interactions of plants, cyst nematodes and soil microbial communities. We conclude that the interactions between the studied organisms do not necessarily depend on their local vs. non-local origin. Nevertheless, we were able to show that local variation in soil organism community composition can be an important factor in determining the outcome of interactions in belowground multitrophic systems.

Soil microorganisms in coastal foredunes control the ectoparasitic root‐feeding nematodeTylenchorhynchus ventralisby local interactions

1 In natural grassland ecosystems, root-feeding nematodes and insects are the dominant below-ground herbivores. In coastal foredunes, the ectoparasitic nematode Tylenchorhynchus ventralis would be a major root herbivore if not strongly controlled by soil microorganisms. Here, we examined if the suppressive effects of the microbial enemies of T. ventralis act by local interactions such as predation, parasitism or antagonism, or local induction of plant defence, or by non-local interactions, such as systemic effects when microorganisms in one section of the plant roots can affect nematode control in another section of the root system. We show that abundance of T. ventralis in the root zone of the grass Ammophila arenaria is suppressed by local interactions. 2 We compared local vs. non-local control of nematodes by a natural community of soil microorganisms in a split-root experiment, where nematodes and microbes were inoculated to the same, or to opposite root compartments. 3 The split-root experiment revealed that microorganisms affected T. ventralis numbers only when present in the same root compartment. Therefore, the effects of microorganisms on T. ventralis are due to local interactions and not due to induction of a systemic defence mechanism in the plant host. 4 When inoculated together with microorganisms, the nematodes were heavily infected with unknown bacteria and with fungi that resembled the genus Catenaria, suggesting that microorganisms control nematodes through parasitism. However, local defence induction cannot be completely excluded. 5 Besides microbial enemies of nematodes, the root zone of A. arenaria also contains plant pathogens. Root biomass was reduced by nematode infection, but also by the combination of nematodes and microorganisms, most likely because the soil pathogens overwhelmed the effects of nematode control on plant production. 6 We conclude that there may be a trade-off between beneficial effects of soil microorganisms on the plant host due to nematode control vs. pathogenic effects of soil microorganisms on the plant host. We propose that such trade-offs require more attention when studying below-ground multitrophic interactions.

Plant ectoparasitic nematodes prefer roots without their microbial enemies

Root-feeding nematodes are major soil-borne pests in agriculture. In natural ecosystems, their abundance can be strongly controlled by natural enemies. In coastal foredune soil, the abundance of the ectoparasitic nematode Tylenchorhynchus ventralis is controlled by local interactions with soil microorganisms. If not controlled, T. ventralis reduces growth and performance of the host plant Ammophila arenaria. In the present study, we examine if the nematodes may sense the presence of soil microorganisms and, if so, they are able to actively avoid their enemies. First, using Petri dishes with agar medium we examined if T. ventralis can choose between A. arenaria seedlings inoculated with or without soil microorganisms. We observed that there was a trend (although non-significant) in nematode migration towards the non-inoculated plants. If the seedlings were not present, the nematodes did not make any choice and stayed in the centre of the Petri dish. Then, using Y-tubes filled with sterilized dune soil, we examined if T. ventralis could choose between A. arenaria roots with or without microorganisms. We also included treatments of microbial suspensions without plants and a microbe-free filtrate. We observed that the nematodes preferred roots without microorganisms. Microorganisms alone or roots with microbial filtrate did not influence nematode choice significantly. We conclude that the nematode T. ventralis is able to choose roots without soil microorganisms when having roots with them as alternative. Such avoidance could explain why biological control of nematodes in field is not always effective, especially when microbial antagonists accumulate in specific parts of the rhizosphere.

Skin Structure and Function

The skin serves as a wall-like barrier to separate and protect the inside of our body from the microbial enemies of the environment and provide a primary defense against infection. The layers of the skin, like the outer wall and secondary inner walls surrounding a medieval city, not only provide protection from external enemies, but also provide niches where normal flora bacteria and fungi can live and conduct business. The structure of the skin and its antimicrobial properties are presented with a discussion of examples of microbes that overcome these protections to cause disease.

Host impairments in patients with neoplastic diseases.

In the course of evolution nature has provided the normal human individual with an impressive and effective defense system against microbial enemies that eclipses even Star Wars, arguably the most advanced and ingenious defense program ever designed by human beings. On its own, the normal defense system recognizes foreign invaders, alerts the relevant protective mechanisms, launches counterattacks, ceases hostilities as soon as the job is done, and clears up the battlefield, causing only negligible collateral damage. An intact system offers protection against most microbial aggressors through a complex interrelationship of protecting surfaces, cells, and soluble factors.

Yesterday's Triumphs: Today's Problems

During the past 100 years, human society has made astonishing advancements in the knowledge of disease. These have usually come about through tedious research accompanied by persistence and optimism. A large increment of the information acquired has been put to beneficent use in endeavors to identify, treat, prevent, suppress, and eradicate many of the formidable microbial, viral, and parasitic enemies of mankind. In the United States, the results have been amazingly successful. By Herculean efforts and constant vigilance, such fearsome diseases as yellow fever, diphtheria, typhoid fever, smallpox, foot-andmouth disease of cattle, tuberculosis due to Mycobacterium bovis , and more recently poliomyelitis, are virtually extinct. The purpose of this essay is to examine the anachronism that certain infectious diseases continue to threaten the lives of human beings despite knowledge concerning their diagnosis, prophylaxis, and treatment that research has provided. Among these diseases are tuberculosis, rabies, and the venereal diseases, gonorrhea and

Mycology Presents Penicillin

A conservative medical official recently told a technical audience that Penicillin is the most potent agent * * * ever encountered, which produces no bad effects upon the patient. He then listed as conspicuous among microbial enemies of man which respond to penicillin, Gonococcus, Meningococcus, Streptococcus hemolyticus and S. viridans, Pneumococcus, Staphylococcus, Clostridium tetanus and C. Welchii, Corynebacterium diplhtheriae and Actinomyces bovis. Such a list justifies the caption miracle drug put upon it by another medical scholar who is rarely swayed by impulse. I am asked to trace the mycological history of the discovery and development of penicillin to its present place among things worth while. Since there are some misunderstandings as to its early history, the data will be presented in as verifiable order as possible. The first ten years. In 1929, Alexander Fleming reported the discovery and naming of penicillin. The essential facts of this discovery consisted (1) in the observation that a particular mold growing as a contaminant in a culture of Staphylococcus aureus inhibited the bacterium, i.e. that the Staphylococcus could not grow in a zone surrounding the mold colony. This observation was already well known as a phenomenon seen frequently when molds and bacteria are found growing together. Most commonly the observation is reversed-a mold fails to develop normally, if at all, in the presence of large numbers of bacteria. (2) Fleming went further and showed that the mold had produced an inhibiting substance in the nutrient substratum which could be separated from the fungus itself and used to inhibit certain bacteria. He tabulated a series of bacteria susceptible and other bacteria resistant to the inhibiting substance. (3) Since the mold was a species of the great genus Penicillium, he called his inhibiting substance penicillin. (4) Not being a mycologist, he undertook to